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Sugar transaminase from a metagenome collected from troll oil field production water
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.2 291 0.2 M Lithium Sulfate,0.1 M Phosphate, 20% w/v PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.405 α = 90 b = 76.405 β = 90 c = 134.44 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.43 59.37 100 0.045 0.999 15.9 8.2 84599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.45 100 2.873 0.282 0.6 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3BN1 1.43 59.37 84532 4195 99.969 0.167 0.1651 0.1973 0.1978 34.673
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.465 0.232 0.465 -1.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.5 r_dihedral_angle_4_deg 19.732 r_dihedral_angle_3_deg 15.281 r_scangle_it 10.262 r_scangle_other 10.26 r_lrange_it 9.786 r_lrange_other 9.754 r_scbond_it 8.55 r_scbond_other 8.548 r_dihedral_angle_1_deg 6.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.5 r_dihedral_angle_4_deg 19.732 r_dihedral_angle_3_deg 15.281 r_scangle_it 10.262 r_scangle_other 10.26 r_lrange_it 9.786 r_lrange_other 9.754 r_scbond_it 8.55 r_scbond_other 8.548 r_dihedral_angle_1_deg 6.274 r_mcangle_other 6.118 r_mcangle_it 6.111 r_mcbond_it 5.933 r_mcbond_other 5.907 r_angle_refined_deg 2.019 r_angle_other_deg 1.479 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.223 r_symmetry_nbd_refined 0.207 r_nbd_other 0.193 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.059 r_xyhbond_nbd_other 0.047 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2927 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building MoRDa phasing